Contacts of the strand formed by residues 487 - 493 (chain A) in PDB entry 2PFP
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 487 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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382A ASP* 4.6 3.7 + - - -
383A PHE* 4.7 2.0 - - - -
385A GLU* 4.0 32.9 + - - +
386A ARG 4.1 5.7 + - - -
387A MET* 3.6 40.4 - - + +
388A PRO* 4.5 3.4 - - - +
391A GLU* 2.9 40.0 + - - +
395A ILE* 4.0 21.5 - - + -
426A GLY 5.9 0.4 - - - -
476A VAL* 3.3 6.7 - - - -
477A CYS* 2.7 40.3 + - - +
478A ARG* 5.7 0.7 - - - -
479A LEU* 6.3 0.7 - - + +
485A ARG* 3.6 34.1 + - - +
486A HIS* 1.3 82.1 + - - +
488A ARG* 1.3 63.9 + - - +
489A LEU 3.6 0.2 + - - -
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Residues in contact with ARG 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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342A TRP* 3.2 23.4 - - + +
383A PHE* 3.7 42.9 - - + +
426A GLY 4.5 6.6 + - - +
427A ASP* 3.1 26.9 + - + +
428A VAL* 3.0 25.1 + - - +
461A LEU* 3.7 22.3 - - - +
474A LEU* 4.2 2.0 - - - +
475A GLY 3.1 27.3 + - - +
476A VAL* 4.6 0.2 - - - +
477A CYS* 5.3 0.2 - - - -
487A ARG* 1.3 76.6 - - - +
489A LEU* 1.3 63.9 + - - +
490A ASP* 2.6 37.3 + - - -
6P C 2.8 30.1 + - - -
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Residues in contact with LEU 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ILE* 4.0 19.5 - - + -
399A VAL* 3.9 11.0 - - + -
428A VAL* 3.5 17.9 - - + +
430A VAL* 4.1 9.9 - - + -
451A LEU* 5.0 0.4 - - + -
456A PHE* 3.9 20.6 - - + -
457A LEU* 3.9 27.6 - - + -
473A TYR* 3.7 4.1 - - + +
474A LEU* 3.5 0.5 - - - -
475A GLY 2.7 48.2 + - - +
476A VAL 5.0 0.2 - - - +
477A CYS* 4.1 14.4 - - + -
487A ARG 3.6 0.4 + - - -
488A ARG* 1.3 73.3 - - - +
490A ASP* 1.3 64.9 + - - +
491A ILE* 4.0 24.2 - - + -
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Residues in contact with ASP 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427A ASP* 3.8 2.5 - - - -
428A VAL 2.9 7.7 + - - +
429A ASP* 3.5 13.2 - - - +
430A VAL* 2.8 26.9 + - - +
473A TYR 3.3 3.8 - - - -
474A LEU* 3.4 18.1 - - + +
488A ARG* 2.6 35.9 + - - -
489A LEU* 1.3 72.1 - - - +
491A ILE* 1.3 64.5 + - - +
492A ILE* 5.9 0.4 - - + -
506A PHE* 4.1 8.0 - - + -
751A NA 2.6 24.7 - - - -
6P C 2.7 27.3 - - - +
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Residues in contact with ILE 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A VAL* 4.0 20.6 - - + -
430A VAL* 3.3 15.3 - - + +
432A ILE* 3.8 24.0 - - + -
444A PHE* 3.6 14.4 - - + -
447A LEU* 4.2 12.6 - - + -
448A LEU* 4.8 4.0 - - + -
451A LEU* 4.5 7.2 - - + -
472A LYS* 3.2 4.0 - - - +
473A TYR* 2.7 57.2 + - + +
474A LEU* 4.9 0.4 - - - +
489A LEU* 4.0 29.8 - - + -
490A ASP* 1.3 80.8 - - - +
492A ILE* 1.3 69.7 + - - +
493A VAL* 4.7 0.7 - - + -
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Residues in contact with ILE 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430A VAL 3.0 7.8 + - - +
431A LEU* 3.3 26.6 - - + -
432A ILE* 2.8 28.1 + - - +
471A GLN 3.3 7.9 - - - +
472A LYS* 4.0 18.6 - - + -
474A LEU* 6.1 1.1 - - + -
490A ASP* 5.9 0.7 - - + -
491A ILE* 1.3 80.5 - - - +
493A VAL* 1.3 61.7 + - - +
494A VAL* 4.1 12.3 - - + -
502A ALA* 4.5 6.1 - - + +
505A TYR* 4.6 11.4 - - + -
506A PHE* 3.6 50.3 - - + -
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Residues in contact with VAL 493 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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432A ILE* 3.2 20.4 - - + +
440A HIS* 3.1 38.7 - - + +
443A ILE* 3.5 29.4 - - + -
444A PHE* 3.4 36.3 - - + -
447A LEU* 5.7 0.9 - - + -
470A GLN 5.0 1.4 - - - +
471A GLN* 3.2 22.5 + - - +
491A ILE* 4.7 0.9 - - + -
492A ILE* 1.3 74.8 - - - +
494A VAL* 1.3 66.2 + - - +
495A PRO* 4.6 1.4 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il